Spider-Man: Origins to Avenger
by Karrio
Summary: Took this down as I didn't like where the story was headed. Anyways, set in the MCU (Before Civil War). Another Origin Story, though this includes Agents of Shield and the Avengers.
1. Chapter 1 - Prologue

**Spider Man: Origins**

 **Prologue**

 **2004**

Lightning crackled in the sky. Right after that, a single thunder roared in the sky and the holes in heaven opened up. Almost instantly, it began to pour. Another shot of lightning and another round of roaring thunder can be heard as a private jet flew over the Atlantic Ocean. They were on there way to London, They left New York about 3 hours ago.

Sitting and staring out the window, the black haired female shifted slightly in her seat. She had to adjust her position as she kept an eye on the storm. She hardly batted an eye as her partner sat across from her. He kept a neutral expression, but Mary knew her husband very well. He was worried about something, and if it's what she thinks it is, they were both in trouble. Keeping his voice low and acting natural, Richard remarked to his wife.

"Something is wrong here. We need to get word to HQ," he said as he picked up a newspaper. He kept his eyes on the pages and his voice low, but he kept his senses on high.

"I know. I have been trying to contact him, but can't get through. I have a feeling they have a jammer on this plane," Mary replied, still looking out the window. She kept an eye on the reflection though. She was on full alert as well.

"I will try and disable it. You will only have a very small window to send that message," Richard stated. He put his paper and in a normal voice, he spoke to his wife. "Going to the bathroom."

He got up and stepped towards the bathroom, while keeping an eye on the other 4 agents on the plane. As he was walking towards the bathroom, he took out his phone. He tried to act casual but the fact the other 4 people knew there was a jammer active gave him away. In a flash, he kicked the nearest agent in the solar plex, which dropped him very quickly. He spotted the jammer in the corner and dove for it. He managed to unplug it before the other agents quickly subdued him.

Meanwhile, when Richard got up, Mary quietly got out her phone, keeping an eye on the other 4 people as well. She knew, once Richard managed to disable the jammer, there will be a very small window to send her message. She brought it out on her phone and was prepared to hit send. She had this message prerecorded earlier, in case this situation ever arised. It was only a few seconds before Richard had gain the attention and cut the jammer. She hit send and saw it was sent successfully. She sprang up from her seat and joined in the fray.

She grabbed one of the agents and threw him off Richard. She grabbed another one as Richard bucked his back, sending the reminder off him. Mary managed to knock one out with a swift kick to the head, and Richard sent one into a coma with a punch to the head. That left 2 still conscious. Before anyone could move, the plane was suddenly hit with something and soon burst into flames. It began a steep dive into the Altantic Ocean. The door opened and 2 people parachuted out of the plane, though there was nowhere for them to go. Both the plane and the 2 survivors hit the water.

 **2013 – AM (After Captain America First Solider)**

It has been a few years since Captain America was thawed out. He was still getting used to the new age but since then, he joined a team of Super Heroes and protected the world from an invasion. He was currently standing in Stark's Tower, which was being renamed the Avengers Tower soon, reading over some files. He placed the files on the table and went to the window and stared across the New York Cityline. This was his city to protect now. A voice suddenly spoke behind him.

"Enjoying the view Rogers?" asked Nick Fury, Director of SHIELD. Captain America, or Steve Rogers if you would, didn't quite trust Fury after learning about the weapons of mass destruction, though he understood why they were designed. He slowly turned around towards the doorway.

"You can say that I suppose," he answered. He stood in a rigid posture. It was just a habit of his. "Do you have an assignment Sir?"

"What? No offer for a coffee?" Fury asked halfheartedly. He knew Rogers wouldn't offer him a cup. He was quite aware of his mistrust. After no response, he continued. "There is something I want you to do."

He walked into the room and placed down 1 file on the desk. Steve, curious now, came over and picked them up. The first thing he noticed was that these were CIA files. With a questionably look at Fury, Captain America asked his question.

"Sir, these aren't SHIELD files. Why are you giving me CIA files?" He wondered out loud. He still opened them and saw 2 names. Richard and Mary Parker. He began to leaf through the files, waiting for an explanation.

"Simple Rogers," Fury started. "They were double agents. They were assigned to spy on.."

"Hydra," Steve finished the statement. He was reading that section of the file now. "It says there plane was destroyed. Rumor has it that The Red Skull had ordered them to be killed, though there wasn't any evidence to verify that. Also states, no bodies were found."

"Precisely," Fury confirmed. He held out another file he had kept hidden. He handed Steve the file. Steve took it, though his trust with Fury was dwindling. "They left a son behind. Peter is his name.. Actually, he lives in Queens. I am worried for the boy. With Hydra starting to show themselves again, he could be in danger."

"So, you want the Avengers to keep an eye on him?" Steve asked, though he already knew the answer.

"No. Just you. I want you to look after him," Fury stated. He walked to the window and looked over New York City. "I don't want him to know what is happening. I want him to have a normal childhood. Don't interfere with his life, unless if it is needed."

"Understood Sir. I will let nothing happen to him," Rogers vowed. Even if he was slowly losing his trust in Fury, he stands by the oath he sworn to protect the innocent. Whoever this Peter Parker is, he was an innocent bystander. He walked towards the window as well. "Curious, why don't you want the others in on this?"

Fury turned and studied Captain America for a moment. He finally answered.

"I know you will do whatever it takes to finish an assignment. And I know you will take it seriously," Fury responded. He walked towards the door and stopped at the doorway. "You may not trust me but I know you still trust in protecting the innocent." With that, he left the towers.

 **2013 – The BUS (Agents of Shield. Between Yes Man and End of the Beginning. Season 1, Episdes 14 and 15).**

Coulson was seated on The BUS, eating a sandwich. He might not have shown it, but inside, he was anxious. It wasn't everyday Nick Fury, Director of SHIELD makes an appearance with an important mission. Looking up as footsteps enters the kitchen area, he nods at Ward.

"How is she?" Phil asked, taking a bite.

"Tired. She trained hard today. Actually, the past week, she has been training extremely hard. I just hope she won't burn out," Ward voices his concern. He makes a quick sandwich and joins Coulson at the table.

"Skye is a strong person. She will be fine," Coulson responded.

"So what's with you?" Ward asked. He finished his sandwich and placed his dish in the sink.

"Call the team together,"Coulson ordered. He placed his plate in the sink as well. He walked to the cargo area.

Ward looked confused and had just gathering the team when there was a slight bump on The BUS, like someone had just landed a plane. Moments later, Fury had descended and was standing beside Coulson. He began the briefing.

"I have an important mission for your team Phil," he began. He brought up the files on Richard and Mary Parker. "Before we go further, I want no trace of this meeting left. Destroy everything. This is completely off the books mission."

"Understood," Phil confirmed. He was intrigued with this mission. Well, more intrigued then before. Like Steve, the team noticed these were CIA files. "Why are we looking at CIA files?"

"Because of this," Fury commented and brought up the picture of the Red Skull. "As you know, Hydra has came out of hiding." He shuffled the images and the files for Richard and Mary Parker came up. "These two were CIA agents, tasked to bring down the Red Skull. Somehow, he got wind of them and had them presumely killed. There were no bodies."

"Tragic, but what does that have to do with us?" Skye asked. She kinda cowered a little under Fury's gaze but she didn't back down.

Fury brought up Peter's file. "They left behind a boy. Now, I doubt Hydra will know who he has, or who his parents were but all the same. I want this team to keep an eye on him. Keep your distance though. Only reveal yourselfs if he needs help."

Skye was immediately drawn to him. Despite it was just a picture, Skye felt a connection. They both grew up with no immediate family. They both pretty much had to learn to live without their parents. She tuned back to the briefing to hear the rest.

"He lives with his Aunt and Uncle in Queens. He attends Midtown High School." finished Fury.

As soon as he got the team to confirm the mission, Fury left the BUS.


	2. Chapter 1 - Origins Part 1

**A/N:** I know, another Origin story. Boy gets bit by spider, boy gains powers, boy yells at Uncle, boy loses uncle, boy becomes hero xD. I will try and speed up the beginning :). Only reason why I have the beginning is because I am including AoS and the Avengers in it as well. :) You might also reconigze the story, as I did post it before. I took it down since I didn't like where it was heading but now that I got a better handle, I will try and have this updated regularly. Won't follow a set schedule (simply because I hate scheduled updates. Anything can happen to push back updates). Anyways, enjoy :)

Chapter 1 – Origins Part 2

 _Queens, New York_

 _2015_

Peter stretched as he climbed out of bed. He places his feet on the floor but just sits on the edge of the bed. He rolls his right shoulder a little, trying to ease the pain a little. Today, he was gonna help his uncle clean the basement. Not usually something a typical teen did on the weekend but Peter was just happy not to be heading to school for 2 days. Later, though, he has a study group to finish his homework. He pushes himself off the bed and heads for a quick shower. He changed into a simple pair of jeans and a green t-shirt and headed down to the kitchen.

His aunt already laid out a breakfast consisting of pancakes. He smiled at her as he slid into a chair. He grabbed 3 pancakes and poured syrup on them.

"Good morning Aunt May," he greeted her with a smile.

"Someone's in a good mood," remarked his aunt with an amused grin.

"Your cooking tends to do that," Peter answered, while placing a forkful of pancakes into his mouth.

His aunt just smiled. She enjoyed that he liked her cooking. She was about to speak when something on the TV caught their attention. It was a news segment on Steve Rogers.

" _That's right Jim," the reporter was saying. She was standing outside the Norman Oscorps Tower. The NYPD had the place taped off. There was a crowd gathered. "From what we are told, Steve Rogers, or simply known to the world as Captain America, singlehandily stopped a potential robbery. No details on what was being targeted but rumors are swirly around that it was something big." We get a shot of the crowd gathering around. "Unfortunately, we couldn't ask him about it. As soon as he saved the day, he left in a hurry. Something seems to be happening. Back to you Jim."_

Peter dropped his fork and immediately pulled out his phone. He sent Harry, his best friend, a text.

(Peter to Harry): **Harry, are you alright?**

Harry's response came back instantly.

{Harry to Peter): **A little hectic but things are alright. Someone tried to rob my dad's place last night.**

Peter replied.

(Peter to Harry): **Do you need anything?**

Harry messaged him back.

(Harry to Peter): **Thanks for your concern but everything is alright. Spend the day with your uncle. Peter.**

Peter nodded to his phone, even though he knows Harry can't see that, and turned his gaze up to his aunt. He realized his uncle had joined them. He waved at him and resumed eating his pancakes.

"Everything alright with Harry?" Uncle Ben asked. He had his plate almost done.

"Yeah. Sounds like nothing was taken. Anyways, Uncle Ben. Do you mind if I help a little later? " Peter asked. He finished his plate and put his dish in the dishwasher.

"That's fine Peter. I have a few errands I have to do anyways before we clean the basement," his uncle replied. He also has finished his breakfast and put his dishes in the dishwasher as well.

Peter left the room and went upstairs. He brushed his teeth, grabbed his bag, put on a sweater and headed back downstairs. He waved goodbye and left the house.

 _The Playground_

 _Classified Location_

 _2015 (Before Many Heads, One Tale). Sane tune Peter saw the news._

"Sir, you might want to see this," Jemma said, proceeding into the Director's office. She brings her tablet out and presses play. Only when she looked up, she realized she interrupted something. "Sorry Sir. I didn't realize you were busy."

Standing around Director Coulson was Daisy, Mac, Bobby, Hunter, Fitz, and May. They were looking at a table with files on them. Files containing potential recruits for Daisy's team. Phil just smiled at her before turning his attention to the monitor. The same clipped showed as shown in New York. Once it was over, Phil looked concerned.

"Did this just happen?" He asked Jemma.

"From all accounts, it looks like it," Jemma confirmed. She joined the group around the table. She didn't show it, but when Coulson looks concerned, this meant something big happened, or will happen. And when that happens, she is worried for her team.

"What can you tell me about Oscorp Industries?" Coulson asked. He looked at Fitz and Simmons.

"Oscorp Industries deals with experimental science. Probably one of their more known research is cross-species genetics, " Fitz pulled up Norman Osborn on the monitor. "The company is said to ran by Norman Osborn. He has studied electrical engineering and chemistry."

"That's nice to know, but why show us?" Hunter wondered.

"Because I asked her to show me anything unusual in New York," Phil stated.

Hunter looked confused and whispered to Mac and Bobby. "How is this unusual?"

"Before you guys joined us, Fury gave us an order to look after someone in New York," Phil explained.

"Why is this the first time you are mentioning this?" Hunter wanted to know. Both Bobby and Mac had the same question written on their faces.

"Do you really have to ask that?" He remarked. He clearly was referring to Bobby and Mac's keeping secrets.

"Fair point," Bobby said quietly. "But why show us this particular segment? Surely attempted robbery happens all the time in New York."

"Want I want to know is what is Ward doing?" Daisy voiced her concern. "He knows but why hasn't he tried anything?"

"That's my question as well,"Coulson said. He noticed the confused looks on Bobby, Mac and Hunter. He pulled up Richard and May Parker's files. "These were double agents. They were CIA but were tasked to spy on Hydra. Rumor has it that The Red Skull knew and had them personally killed, though no bodies were ever found. They left behind a child. Fury asked us to keep an eye on him."

"But did you just say Ward knew?" Mac asked.

"Yes." Daisy confirmed. "But he has known about Peter for 2 years now yet he hasn't done anything."

"We are hoping it's because Peter doesn't pose a threat to Hydra," Jemma said, with a small hopeful tone.

"But, again, why bring this up?" Hunter asked, not seeing a connection between Norman Osborn and this Peter guy.

"Could be nothing," Phil said. "But I am curious as to what was almost stolen that caught Captain America's attention."

Jemma was looking through the history of the company when a name caught her eye. She dug deeper, and soon found a classified file with the name _Richard Parker_ on it. She brought it up on the monitor. She heard Coulson swear under his breath.

"Guess that clears it up," Hunter remarked.

"I can't crack the code," Jemma uttered. She looked over at Daisy. "Any chance you can?"

Daisy grinned and went to work. It was encrypted well but in a few moments, she had opened the file. Her grin faltered when she saw it was empty. She looked over at Coulson.

"Why would they classify an empty file?" He was wondering, though he knew perfectly well. Someone had covered up and buried this file. "We need to get to the bottom of this. Mac, Fitz and Hunter, I want you guys to go examine the scene. Find anything you can. Simmons, I want you to pose as an exchange student and gain entry into that building. We need to know what they are doing."

"You are sending me in alone?" Jemma asked. Her voice was half afraid, but half excited to have a solo mission.

"No. Bobby will be with you. She can be your guide while in New York." He answered. "We need to keep a closer eye on Peter. Even though Ward, or Hydra, hasn't tried anything, doesn't mean they won't. Someone went to lengths to hide that file. Something tells me he is in danger," He

"I don't think that's a good idea Phil," May objected.

"Why not?" He wanted to know.

"We don't know anything. We don't even know if the two events are related. And you said so yourself. Ward hasn't tried anything in the last 2 years. Why would he do anything now?" May pointed out.

"I know. But this can't be a coincidence," he retorted.

"What do you want us to do Sir?" Daisy interjected.

"I want you to scour through the files and if you can find anything. There's not much we can do until then," He commented. "We all have our duties. Gear up and meet on the BUS in 30 minutes."


	3. Chapter 1 - Origins Part 2

**Chapter 1 – Origins Part 3**

 _Queens, New York_

 _2015_

Peter returned a few hours later and joined his uncle in the basement. For a good solid hour, Pete and Uncle Ben began organizing boxes in piles. Pile 1 was to keep, pile 2 was to throw away, pile 3 was to go through them and see what has been hiding. Soon, the box piles had grown considerably. All the while, Uncle Ben had been thinking about a few things. He finally managed to talk.

"How's school going Peter?" he asked, pulling a box down from the top shelf. He opened the box and began to take out the contents.

"Alright I guess," Peter answered, also grabbing a box from the top shelf. He opened it and began going through it.

"You sure? You know, if there is any trouble, you can talk to us," his uncle replied. He put this box in the discard pile and grabbed another one.

"I will come to you if there is trouble," Peter reassured him. He also put his box in the discard pile and grabbed a new one.

"Well then, tell me about your right shoulder," Uncle Ben commanded. He noticed Peter looking shocked and chuckled a little. "I know a bruise from fighting when I see it. Since the school hasn't called me, you haven't been getting into fights but something is going on."

"It's fine," Peter replied. His voice wavered a little. "Nothing I can't handle."

Uncle Ben studied his nephew for a moment and then nodded. He was concerned for him, but he trusts Peter. He was about to change his question when he grabbed another box. He opened the box and realized this is his brother's. He saw Peter looking and handed the box to him.

"I didn't realize he kept this box," he said. He turned back and took down another box. "He has kept it since his college days."

Pete began to go through the box. It had his college jacket, his diploma, pictures of Richard, Mary, Uncle Ben and Aunt May, a couple of medals and science book. Pete closed the lid and placed it to the side. He was going to take it to his room later. He looked down at the time and realized he was running late. He snapped out his phone and sent a text to Harry. He then looked at his uncle with an apologetic look.

"Sorry Uncle Ben. I do have to leave. I am a few minutes late to finish our homework assignment," Peter explained. With a nod from his uncle, Peter left the room, grabbed his board and bag and skated towards the library.

 _ **Manhattan, New York**_

 _Oscorp's Industries_

Fitz stood at the scene with his hands on his shirt. Hunter, Mac and him scoured the entire place but no trace on what was almost stolen. It was as if someone scrapped the spot with bleach. They left nothing behind. Not even a single strain of hair. He realized that Hunter was talking to him and turned his attention to him.

"You there mate?" he asked. He was standing beside Mac.

"Yeah. Sorry. Just thinking. This doesn't make sense. This is the exact spot where the attempted robbery happened but there is no sign anything took place," Fitz sounded annoyed.

"Someone is sure trying to cover something," Mac observed.

"Yes but why?" Hunter posed the question. "Do you think Hydra is really behind it?"

"It anything weird happens, I will always suspect Hydra," Mac responded.

"But why try to rob Oscorp?" Fitz asked.

Hunter was about to respond when 6 guys rushed the group. 2 guys grabbed Mac from behind, 2 charged Hunter and 2 sprinted towards Fitz.

Mac spun on his heel and elbowed the first guy in the jaw. Once he heard the satisifying crunch, he grabbed the second guy and throw him over his right shoulder. The first guy tried to push his luck and came at Mac with his fists ready. But Mac was ready as well. He shifted his weight forward as he threw a jab to the man's face and watching as the guy crumples. He joined his friend in lalaland and Mac looked up to see how his comrades were fairing.

Hunter tried to draw his gun but didn't have time. He felt the blow smash his face. Reflexes kicked in as Hunter sent a haymaker towards the guy on the left. It stunned him for a second, which was enough time for him to send a left uppercut to the chin of the 2nd guy. That manages to bring the guy to his knees. Hunter sends a swift kick to the guy's face, knocking him unconcious. He shifted his attention to the first guy. He saw him charging him and planted his feet. He ducked the punch, came up with a knee to the solar plexus. That instantly dropped that guy. He then turned his attention to Fitz.

Fitz, not having a lot of experience in fighting, was holding his own pretty well. He managed to subdue the first guy with a kick to the shin, then a knee to the face. He only had one guy left to face. His adrenaline was pumping but he made a mistake. He went in for a right hook in which the guy sidesteps the punch and gets Fitz into a headlock. He was slowly pushing on his windpipes. His vision was losing focus when suddenly the pressure had lifted. He was gasping for air as Hunter helped him up. As Fitz's vision was returning, he saw the guy was knocked out. A few moments later, they had gathered each other.

"What now?" Hunter wanted to know. "Should we take one of these guys for questioning?"

"We need to regroup. As much as I want to, we can't risk it," Fitz answered. He was still a little lightheaded but was regaining his strength. He looked down at the bodies on the street. Only then, he realized there was a crowd and they seemed very surprised at the fight. He noticed people taking photos with their phones. He looked at Mac and Hunter silently indicted they should leave.


End file.
